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Journal articles on the topic 'Arginine clusters'

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Author: Grafiati
Published: 6 September 2023

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1

Horbal, Liliya, Marc Stierhof, Anja Palusczak, Nikolas Eckert, Josef Zapp, and Andriy Luzhetskyy. "Cyclofaulknamycin with the Rare Amino Acid D-capreomycidine Isolated from a Well-Characterized Streptomyces albus Strain." Microorganisms 9, no. 8 (July 28, 2021): 1609. http://dx.doi.org/10.3390/microorganisms9081609.

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Targeted genome mining is an efficient method of biosynthetic gene cluster prioritization within constantly growing genome databases. Using two capreomycidine biosynthesis genes, alpha-ketoglutarate-dependent arginine beta-hydroxylase and pyridoxal-phosphate-dependent aminotransferase, we identified two types of clusters: one type containing both genes involved in the biosynthesis of the abovementioned moiety, and other clusters including only arginine hydroxylase. Detailed analysis of one of the clusters, the flk cluster from Streptomyces albus, led to the identification of a cyclic peptide that contains a rare D-capreomycidine moiety for the first time. The absence of the pyridoxal-phosphate-dependent aminotransferase gene in the flk cluster is compensated by the XNR_1347 gene in the S. albus genome, whose product is responsible for biosynthesis of the abovementioned nonproteinogenic amino acid. Herein, we report the structure of cyclofaulknamycin and the characteristics of its biosynthetic gene cluster, biosynthesis and bioactivity profile.
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2

Shaikh, A. R., and D. Shah. "Arginine-Amino Acid Interactions and Implications to Protein Solubility and Aggregation." Journal of Engineering Research [TJER] 12, no. 2 (December 1, 2015): 1. http://dx.doi.org/10.24200/tjer.vol12iss2pp1-14.

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Arginine, useful in protein refolding, solubilization of proteins, and suppression of protein aggregation and non-specific adsorption during formulation and purification, is a ubiquitous additive in the biotechnology and pharmaceutical industries. In order to provide a framework for analyzing the molecular level mechanisms behind arginine/protein interactions in the above context, density functional theory was used to systematically examine how arginine interacts with naturally occurring amino acids. The results show that the most favorable interaction of arginine is with acidic amino acids and arises from charge interactions and hydrogen-bond interactions. Arginine is also shown to form stacking and T-shaped structures with aromatic amino acids, the types of cation–p and N–H…p interactions, respectively, known to be important contributors to protein stability. The analysis also shows that arginine-arginine interactions lead to stable clusters, with the stability of the clusters arising from the stacking of the guanidinium part of arginine. The results show that the unique ability of arginine to form clusters with itself makes it an effective aggregation suppressant and support the interpretations of the current study using experimental and molecular dynamics results available in the literature. The results also contribute to understanding the role of arginine in increasing protein solubility, imparting thermal stability of important enzymes, and designing better additives.
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3

Bentham, Matthew, Sabine Mazaleyrat, and Mark Harris. "Role of myristoylation and N-terminal basic residues in membrane association of the human immunodeficiency virus type 1 Nef protein." Journal of General Virology 87, no. 3 (March 1, 2006): 563–71. http://dx.doi.org/10.1099/vir.0.81200-0.

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Human immunodeficiency virus type 1 Nef protein is N-terminally myristoylated, a modification reported to be required for the association of Nef with cytoplasmic membranes. As myristate alone is not sufficient to anchor a protein stably into a membrane, it has been suggested that N-terminal basic residues contribute to Nef membrane association via electrostatic interactions with acidic phospholipids. Here, data are presented pertaining to the role of the myristate and basic residues in Nef membrane association, subcellular localization and function. Firstly, by using a biochemical assay for membrane association it was shown that, whereas myristoylation of Nef was not essential, mutation of a cluster of four arginines between residues 17 and 22 reduced membrane association dramatically. Mutation of two lysines at residues 4 and 7 had negligible effect alone, but when combined with the arginine substitutions, abrogated membrane association completely. By using indirect immunofluorescence, it was demonstrated that mutation of either of the two basic clusters altered the subcellular distribution of Nef dramatically. Thirdly, the requirement of the arginine and lysine clusters for Nef-mediated CD4 downmodulation was shown to correlate precisely with membrane association. These data suggest that membrane localization and subcellular targeting of Nef are controlled by a complex interplay of signals at the N terminus of the protein.
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4

Luo, Xiaomei, and Juncheng Liu. "Transcriptome Analysis of Acid-Responsive Genes and Pathways Involved in Polyamine Regulation in Iron Walnut." Genes 10, no. 8 (August 10, 2019): 605. http://dx.doi.org/10.3390/genes10080605.

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We reported changes in the co-regulated mRNA expression in iron walnut (Juglans sigillata) in response to soil pH treatments and identified mRNAs specific to acidic soil conditions. Phenotypic and physiological analyses revealed that iron walnut growth was greater for the pH 4–5 and pH 5–6 treatments than for the pH 3–4 and pH 6–7 treatments. A total of 2768 differentially expressed genes were detected and categorized into 12 clusters by Short Time-series Expression Miner (STEM). The 994 low-expression genes in cluster III and 255 high-expression genes in cluster X were classified as acid-responsive genes on the basis of the relationships between phenotype, physiology, and STEM clustering, and the two gene clusters were analyzed by a maximum likelihood (ML) evolutionary tree with the greatest log likelihood values. No prominent sub-clusters occurred in cluster III, but three occurred in cluster X. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that acid-responsive genes were related primarily to arginine biosynthesis and the arginine/proline metabolism pathway, implying that polyamine accumulation may enhance iron walnut acid stress tolerance. Overall, our results revealed 1249 potentially acid-responsive genes in iron walnut, indicating that its response to acid stress involves different pathways and activated genes.
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5

Brudar, Sandi, and Barbara Hribar-Lee. "The Effect of Arginine on the Phase Stability of Aqueous Hen Egg-White Lysozyme Solutions." International Journal of Molecular Sciences 24, no. 2 (January 7, 2023): 1197. http://dx.doi.org/10.3390/ijms24021197.

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The effect of arginine on the phase stability of the hen egg-white lysozyme (HEWL) has been studied via molecular dynamics computer simulations, as well as experimentally via cloud-point temperature determination. The experiments show that the addition of arginine increases the stability of the HEWL solutions. The computer simulation results indicate that arginine molecules tend to self-associate. If arginine residues are located on the protein surface, the free arginine molecules stay in their vicinity and prevent the way protein molecules “connect” through them to form clusters. The results are not sensitive to a particular force field and suggest a possible microscopic mechanism of the stabilizing role of arginine as an excipient.
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6

Kohbara, J., W. Michel, and J. Caprio. "Responses of single facial taste fibers in the channel catfish, Ictalurus punctatus, to amino acids." Journal of Neurophysiology 68, no. 4 (October 1, 1992): 1012–26. http://dx.doi.org/10.1152/jn.1992.68.4.1012.

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1. Amino acids and nucleotides stimulate taste receptors of teleosts. In this report, responses to these compounds of 105 facial taste fibers (79 fully characterized) that innervate maxillary barbel taste buds of the channel catfish (Ictalurus punctatus) were analyzed. 2. The fully characterized facial taste fibers that responded to amino acids (n = 68) were generally poorly responsive to nucleotides and related substances (NRS), whereas the fibers responsive to NRS (n = 11) were poorly responsive to amino acids. Spike discharge of the amino acid-responsive fibers to the most potent amino acid stimulus tested per fiber increased 44-fold from a mean spontaneous activity of 2.1 +/- 3.5 to 92.1 +/- 42.4 (SD) spikes/3 s. Spike activity of the NRS-responsive fibers to NRS increased 11.5-fold from a mean spontaneous activity of 3.4 +/- 5.9 to 39.1 +/- 27.4 spikes/3 s. There was no significant difference between the spontaneous rates, but stimulus evoked spike rates for the amino acid-responsive fibers were significantly greater (P < 0.05; Mann-Whitney test) than those for the NRS-responsive fibers. 3. Hierarchical cluster analysis based on the 3-s response time identified three major groups of neurons. The identified clusters comprised neurons that were highly responsive to either L-alanine (i.e., Ala cluster; n = 39), L-arginine (i.e., Arg cluster; n = 29), or NRS (NRS cluster; n = 11). Fibers comprising the Arg cluster were more narrowly tuned than those within the Ala cluster. This report further characterizes the responses to amino acids of the individual facial taste fibers comprising the Ala and Arg clusters. 4. Subclusters were evident within both of the amino acid-responsive clusters. The Arg cluster was divisible into two subclusters dependent on the response to 1 mM L-proline. Twelve neurons that were significantly (P < 0.05; Mann-Whitney test) more responsive to L-proline than the remaining 17 neurons within the Arg cluster formed the Arg/Pro subcluster; these latter 17 neurons comprised the Arg subcluster. However, there was no significant difference (Mann-Whitney test) in the response to L-arginine between fibers within either subcluster across four different response times analyzed. Fibers within the Ala cluster were generally poorly responsive to L-proline. Four alanine subclusters were suggested on the basis of their relative responses to L-alanine, D-alanine, L-arginine, and the NRS; however, of the 39 fibers comprising the alanine cluster, two alanine subclusters comprised only two fibers each, and the third subcluster consisted of four fibers.(ABSTRACT TRUNCATED AT 400 WORDS)
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7

Smart, W. C., J. A. Coffman, and T. G. Cooper. "Combinatorial regulation of the Saccharomyces cerevisiae CAR1 (arginase) promoter in response to multiple environmental signals." Molecular and Cellular Biology 16, no. 10 (October 1996): 5876–87. http://dx.doi.org/10.1128/mcb.16.10.5876.

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CAR1 (arginase) gene expression responds to multiple environmental signals; expression is induced in response to the intracellular accumulation of arginine and repressed when readily transported and catabolized nitrogen sources are available in the environment. Up to 14 cis-acting sites and 9 trans-acting factors have been implicated in regulated CAR1 transcription. In all but one case, the sites are redundant. To test whether these sites actually participate in CAR1 expression, each class of sites was inactivated by substitution mutations that retained the native spacing of the CAR1 cis-acting elements. Three types of sites function independently of the nitrogen source: two clusters of Abflp- and Rap1p-binding sites, and a GC-rich sequence. Two different sets of nitrogen source-dependent sites are also required: the first consists of two GATAA-containing UASNTR sites that mediate nitrogen catabolite repression-sensitive transcription, and the second is arginine dependent and consists of three UAS1 elements that activate transcription only when arginine is present. A single URS1 site mediates repression of CAR1 arginine-independent upstream activator site (UAS) activity in the absence of arginine and the presence of a poor nitrogen source (a condition under which the inducer-independent Gln3p can function in association with the UASNTR sites). When arginine is present, the combined activity of the UAS elements overcomes the negative effects mediated by URS1. Mutation of the classes of sites either singly or in combination markedly alters CAR1 promoter operation and control, supporting the idea that they function synergistically to regulate expression of the gene.
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8

Smart, Scott E., Viktor Dubovoy, and Long Pan. "Stabilization of cationic aluminum hydroxide clusters in high pH environments with a CaCl2/l-arginine matrix." Chemical Communications 55, no. 43 (2019): 5998–6001. http://dx.doi.org/10.1039/c9cc01463b.

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9

Nam, Yong-Suk, Ana Petrovic, Kyu-Shik Jeong, and Sundararajan Venkatesan. "Exchange of the Basic Domain of Human Immunodeficiency Virus Type 1 Rev for a Polyarginine Stretch Expands the RNA Binding Specificity, and a Minimal Arginine Cluster Is Required for Optimal RRE RNA Binding Affinity, Nuclear Accumulation, andtrans-Activation." Journal of Virology 75, no. 6 (March 15, 2001): 2957–71. http://dx.doi.org/10.1128/jvi.75.6.2957-2971.2001.

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ABSTRACT The Rev regulatory protein of human immunodeficiency virus (HIV) facilitates the nuclear export of unspliced and partially spliced HIV RNAs. Using a Rev:MS2 phage coat protein fusion that could be targeted to bind and activate the Rev-responsive element (RRE) RNA or heterologous MS2 phage operator RNA, we analyzed the role(s) of the arginine-rich RNA binding domain in RNA binding and transactivation. The arginine-rich domain could be functionally replaced by a stretch of nine arginines. However, polyarginine substitutions expanded the RNA binding specificity of the resultant mutant Rev protein. Polyarginine insertions in place of residues 24 to 60 that excised the RNA binding and oligomerization domains of Rev preserved the activation for MS2 RNA, but not for the RRE. A nine-arginine insertion outside of the natural context of the Rev nuclear localization signal domain was incompatible with activation of either RNA target. Insertions of fewer than eight arginines impaired RRE activation. Interrupted lysine clusters and disruption of the arginine stretch with lysine or neutral residues resulted in a similar phenotype. Some of these mutants with a null phenotype for RRE activated the heterologous MS2 RNA target. Under steady-state conditions, mutants that preserved the Rev response for RRE RNA localized to the nuclei; those with poor or no Rev response accumulated mostly in the cytoplasm. Many of the cytoplasmically resident derivatives became nuclear when leptomycin B (LMB) treatment inhibited nuclear export of nuclear export signal-containing proteins. Mutants that had a null activation potential for either RNA target were particularly resistant to LMB treatment. Abbreviated nuclear residence times and differences in RRE binding affinity may have compromised their activation potential for RRE. High-affinity binding to MS2 RNA through the intact coat protein was sufficient to overcome the short nuclear residence times and to facilitate MS2 activation by some derivatives.
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10

Ghiasi, Mina, Shadi Bavafa, and Mansour Zahedi. "QM study of interaction between arginine amino acid and Au clusters and the effects on arginine acidity." Gold Bulletin 54, no. 1 (January 22, 2021): 45–57. http://dx.doi.org/10.1007/s13404-021-00292-7.

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11

Nielsen, T. B., K. B. Yderstraede, H. D. Schrøder, Jens Juul Holst, Klaus Brusgaard, and H. Beck-Nielsen. "Functional and Immunohistochemical Evaluation of Porcine Neonatal Islet-Like Cell Clusters." Cell Transplantation 12, no. 1 (January 2003): 13–25. http://dx.doi.org/10.3727/000000003783985142.

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Porcine neonatal islet-like cell clusters (NICCs) may be an attractive source of insulin-producing tissue for xenotransplantation in type I diabetic patients. We examined the functional and immunohistochemical outcome of the islet grafts in vitro during long-term culture and in vivo after transplantation to athymic nude mice. On average we obtained 29,000 NICCs from each pancreas. In a perifusion system, NICCs responded poorly to a glucose challenge alone, but 10 mmol/L arginine elicited a fourfold increase in insulin secretion and 16.7 mmol/L glucose + 10 mmol/L arginine caused a sevenfold increase in insulin secretion, indicating some sensitivity towards glucose. Hormone content as well as the number of hormone-containing cells increased for the first 14 days of culture. When NICCs were stained for hormones, proliferation (Ki67), and duct cells (CK7), some insulin- and glucagon-positive cells co-stained for proliferation. However no co-staining was observed between insulin- and glucagon-positive cells or between hormone- and CK7-positive cells. Following transplantation of 2000 NICCs under the renal capsule of diabetic nude mice, BG levels were normalized within an average of 13 weeks. Oral and IP glucose tolerance tests revealed a normal or even faster clearance of a glucose load compared with normal controls. Immunohistochemical examination of the grafts revealed primarily insulin-positive cells. In summary, in vitro, NICCs responded to a challenge including glucose and arginine. There was a potential for expansion of the β-cell mass of NICCs in vitro as well as in vivo where NICCs eventually may normalize blood glucose of diabetic mice.
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12

Wu, Qiong, Jing Lu, Xiao Lin Ji, Tao Yu Zou, Zhen Fang Qiao, Hong Ping Ju, and Hai Wang. "A New Organic-Inorganic Hybrid Based on L-Arginine and Polyoxoanion." Advanced Materials Research 1105 (May 2015): 335–38. http://dx.doi.org/10.4028/www.scientific.net/amr.1105.335.

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Modifying polyoxometalates with organic and/or metal-organic moieties is a widely adopted method for broading the range of properties. In this work a new polyoxometalate constructed from Anderson-type polyoxoanions and L-arginine (Arg =L-arginine) molecules Na [CrMo6(OH)6O18]}(H2Arg)2·8H2O(1) has been synthesized via conventional method and characterized by routine techniques. Single-crystal X-Ray diffraction analysis shows that compound 1 is constructed by chiralL-arginine grafted Anderson-type clusters, sodium cation and water molecules which are further stabilized by hydrogen bonding interactions constitute 3D supramolecular networks. In addition, both antitumor behavior and photocatalytic activities of compound 1 were investigated.
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13

Yang, David S., Arash Saeedi, Aram Davtyan, Mohsen Fathi, Michael B. Sherman, Mohammad S. Safari, Alena Klindziuk, et al. "Mesoscopic protein-rich clusters host the nucleation of mutant p53 amyloid fibrils." Proceedings of the National Academy of Sciences 118, no. 10 (March 2, 2021): e2015618118. http://dx.doi.org/10.1073/pnas.2015618118.

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The protein p53 is a crucial tumor suppressor, often called “the guardian of the genome”; however, mutations transform p53 into a powerful cancer promoter. The oncogenic capacity of mutant p53 has been ascribed to enhanced propensity to fibrillize and recruit other cancer fighting proteins in the fibrils, yet the pathways of fibril nucleation and growth remain obscure. Here, we combine immunofluorescence three-dimensional confocal microscopy of human breast cancer cells with light scattering and transmission electron microscopy of solutions of the purified protein and molecular simulations to illuminate the mechanisms of phase transformations across multiple length scales, from cellular to molecular. We report that the p53 mutant R248Q (R, arginine; Q, glutamine) forms, both in cancer cells and in solutions, a condensate with unique properties, mesoscopic protein-rich clusters. The clusters dramatically diverge from other protein condensates. The cluster sizes are decoupled from the total cluster population volume and independent of the p53 concentration and the solution concentration at equilibrium with the clusters varies. We demonstrate that the clusters carry out a crucial biological function: they host and facilitate the nucleation of amyloid fibrils. We demonstrate that the p53 clusters are driven by structural destabilization of the core domain and not by interactions of its extensive unstructured region, in contradistinction to the dense liquids typical of disordered and partially disordered proteins. Two-step nucleation of mutant p53 amyloids suggests means to control fibrillization and the associated pathologies through modifying the cluster characteristics. Our findings exemplify interactions between distinct protein phases that activate complex physicochemical mechanisms operating in biological systems.
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14

Martin-Kearley, Jennifer, John A. Gow, Marc Péloquin, and Charles W. Greer. "Numerical analysis and the application of random amplified polymorphic DNA polymerase chain reaction to the differentiation of Vibrio strains from a seasonally cold ocean." Canadian Journal of Microbiology 40, no. 6 (June 1, 1994): 446–55. http://dx.doi.org/10.1139/m94-073.

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Eighty regional strains of Vibrio isolated from the seasonally cold waters of coastal Newfoundland, and a number of Vibrio reference cultures, were studied. The regional strains had been isolated from the brown macroalga Alaria esculenta and the giant scallop Placopecten magellanicus and were known to grow at 4 °C. The strains were grouped according to their arginine-dihydrolase reactions and examined by numerical analysis. According to phenotypic properties the arginine-dihydrolase positive strains closely resembled Vibrio splendidus biovar I. Most clusters of the arginine-dihydrolase negative strains appeared to be unique but the closest phenotypic resemblance among some strains was with Vibrio ordalii. Some strains were examined using the random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) technique for fingerprinting and it was shown that the regional strains were significantly different from either V. splendidus biovar I or V. ordalii. Generally, the strains from seaweed clustered separately from those that were from scallops. Strains in some clusters, especially those from the seaweed, were able to utilize most of the compounds that were tested as sole sources of carbon and energy.Key words: numerical taxonomy, marine bacteria, Vibrio, psychrotrophs, RAPD-PCR.
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15

Hutcheon, G. W., and A. Bolhuis. "The archaeal twin-arginine translocation pathway." Biochemical Society Transactions 31, no. 3 (June 1, 2003): 686–89. http://dx.doi.org/10.1042/bst0310686.

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The twin-arginine translocation (Tat) pathway is a system with the unique ability to export proteins in a fully folded conformation. Its main components are TatA, TatB and TatC, all of which are required for Tat-dependent export. The Tat pathway is found in several Archaea, and in most of them a moderate number of predicted Tat-dependent substrates are present. Putative substrates include those binding cofactors such as iron–sulphur clusters and molybdopterin. In these Archaea, the role of the Tat pathway seems to be similar to that of bacteria: the export of a small subset of proteins that fold before translocation across the cytoplasmic membrane. The exception to this is the Tat system of the halophilic archaeon Halobacterium sp. NRC-1. In this organism, the majority of extra-cytoplasmic proteins are predicted to use the Tat pathway, which is, most likely, a specific adaptation to its particular lifestyle in highly saline conditions.
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16

Abdollahi, Sara, Mohammad H. Morowvat, Amir Savardashtaki, Cambyz Irajie, Sohrab Najafipour, Mahboubeh Zarei, and Younes Ghasemi. "Amino Acids Sequence-based Analysis of Arginine Deiminase from Different Prokaryotic Organisms: An In Silico Approach." Recent Patents on Biotechnology 14, no. 3 (September 25, 2020): 235–46. http://dx.doi.org/10.2174/1872208314666200324114441.

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Background: Arginine deiminase is a bacterial enzyme, which degrades L-arginine. Some human cancers such as hepatocellular carcinoma (HCC) and melanoma are auxotrophic for arginine. Therefore, PEGylated arginine deiminase (ADI-PEG20) is a good anticancer candidate with antitumor effects. It causes local depletion of L-arginine and growth inhibition in arginineauxotrophic tumor cells. The FDA and EMA have granted orphan status to this drug. Some recently published patents have dealt with this enzyme or its PEGylated form. Objective: Due to increasing attention to it, we aimed to evaluate and compare 30 arginine deiminase proteins from different bacterial species through in silico analysis. Methods: The exploited analyses included the investigation of physicochemical properties, multiple sequence alignment (MSA), motif, superfamily, phylogenetic and 3D comparative analyses of arginine deiminase proteins thorough various bioinformatics tools. Results: The most abundant amino acid in the arginine deiminase proteins is leucine (10.13%) while the least amino acid ratio is cysteine (0.98%). Multiple sequence alignment showed 47 conserved patterns between 30 arginine deiminase amino acid sequences. The results of sequence homology among 30 different groups of arginine deiminase enzymes revealed that all the studied sequences located in amidinotransferase superfamily. Based on the phylogenetic analysis, two major clusters were identified. Considering the results of various in silico studies; we selected the five best candidates for further investigations. The 3D structures of the best five arginine deiminase proteins were generated by the I-TASSER server and PyMOL. The RAMPAGE analysis revealed that 81.4%-91.4%, of the selected sequences, were located in the favored region of arginine deiminase proteins. Conclusion: The results of this study shed light on the basic physicochemical properties of thirty major arginine deiminase sequences. The obtained data could be employed for further in vivo and clinical studies and also for developing the related therapeutic enzymes.
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17

Julian, Ryan R., J. L. Beauchamp, and William A. Goddard. "Cooperative Salt Bridge Stabilization of Gas-Phase Zwitterions in Neutral Arginine Clusters." Journal of Physical Chemistry A 106, no. 1 (January 2002): 32–34. http://dx.doi.org/10.1021/jp013205i.

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18

Zhang, Duxi, Lianming Wu, Kim Koch, and R. Cooks. "Arginine clusters generated by electrospray ionization and identified by tandem mass spectrometry." European Journal of Mass Spectrometry 5, no. 1 (1999): 353. http://dx.doi.org/10.1255/ejms.295.

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19

Bragg, Jennifer N., Diane M. Lawrence, and Andrew O. Jackson. "The N-Terminal 85 Amino Acids of the Barley Stripe Mosaic Virus γb Pathogenesis Protein Contain Three Zinc-Binding Motifs." Journal of Virology 78, no. 14 (July 15, 2004): 7379–91. http://dx.doi.org/10.1128/jvi.78.14.7379-7391.2004.

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ABSTRACT Barley stripe mosaic virus RNAγ encodes γb, a cysteine-rich protein that affects pathogenesis. Nine of the eleven cysteines are concentrated in two clusters, designated C1 (residues 1 to 23) and C2 (residues 60 to 85), that are arranged in zinc finger-like motifs. A basic motif (BM) rich in lysine and arginine (residues 19 to 47) resides between the C1 and C2 clusters. We have demonstrated that γb binds zinc and that the C1, BM, and C2 motifs have independent zinc-binding activities. To evaluate the requirements for binding, mutations were introduced into each region. Cysteine residues at positions 7, 9, 10, 19, and 23 in the C1 motif were replaced with serines. In the BM, asparagines were substituted for lysines at positions 26 and 35, glutamine for arginine at position 25, and glycines for arginines at positions 33 and 36. The C2 mutations included cysteine replacements with serines at positions 60, 64, 71, and 81, and a histidine-to-leucine change at position 85. These mutations destroyed zinc-binding activity in each of the isolated motifs. γb derivatives containing mutations in only two of the motifs retained the ability to bind zinc, whereas a γb derivative containing mutations inactivating all three motifs destroyed the ability to bind zinc. Plants inoculated with transcripts containing combinations of the C1, BM, and C2 mutations elicited a “null” phenotype in barley characteristic of γb deletion mutants and also delayed the appearance and reduced the size of local lesions in Chenopodium amaranticolor. These results show that zinc binding of each of the motifs is critical for the biological activity of γb.
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20

McCorvie, Thomas J., Paula M. Loria, Meihua Tu, Seungil Han, Leela Shrestha, D. Sean Froese, Igor M. Ferreira, Allison P. Berg, and Wyatt W. Yue. "Molecular basis for the regulation of human glycogen synthase by phosphorylation and glucose-6-phosphate." Nature Structural & Molecular Biology 29, no. 7 (July 2022): 628–38. http://dx.doi.org/10.1038/s41594-022-00799-3.

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AbstractGlycogen synthase (GYS1) is the central enzyme in muscle glycogen biosynthesis. GYS1 activity is inhibited by phosphorylation of its amino (N) and carboxyl (C) termini, which is relieved by allosteric activation of glucose-6-phosphate (Glc6P). We present cryo-EM structures at 3.0–4.0 Å resolution of phosphorylated human GYS1, in complex with a minimal interacting region of glycogenin, in the inhibited, activated and catalytically competent states. Phosphorylations of specific terminal residues are sensed by different arginine clusters, locking the GYS1 tetramer in an inhibited state via intersubunit interactions. The Glc6P activator promotes conformational change by disrupting these interactions and increases the flexibility of GYS1, such that it is poised to adopt a catalytically competent state when the sugar donor UDP-glucose (UDP-glc) binds. We also identify an inhibited-like conformation that has not transitioned into the activated state, in which the locking interaction of phosphorylation with the arginine cluster impedes subsequent conformational changes due to Glc6P binding. Our results address longstanding questions regarding the mechanism of human GYS1 regulation.
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21

van Oers, Nicolai, Laura DeFord-Watts, David Dougall, Blake Johnson, Jennifer Eitson, Li Yan, and Christoph Wuelfing. "The TCR CD3 ζ subunit contains a charged inositol phospholipid-binding sequence that supports T cell interactions with antigen presenting cells (50.4)." Journal of Immunology 184, no. 1_Supplement (April 1, 2010): 50.4. http://dx.doi.org/10.4049/jimmunol.184.supp.50.4.

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Abstract TCR-mediated intracellular signal transmission commences following the tyrosine phosphorylation of the CD3-encoded ITAMs. The CD3 ζ subunit, containing three ITAMs per chain, becomes one of the more heavily phosphorylated of the CD3 chains. The cytoplasmic tail of CD3 ζ contains multiple clusters of basic amino acids lysine and arginine. A number of transmembrane and cytosolic proteins, including the CD3 ϵ subunit, use these types of clusters to bind phospholipids. We report that the cytoplasmic tail of CD3 ζ contains a phospholipid-binding cluster with a relatively high affinity for PtdIns(3,5)P2, PtdIns(5)P, PtdIns(3)P, and PtdIns(4)P. The elimination of the phospholipid-binding function of CD3 ζ reduced the stability of TCR clustering at the immunological synapse. The function of this domain in TCR-mediated intracellular signaling responses will be described. These findings demonstrate a novel functional role for the CD3 ζ lipid-binding domain in T cell biology.
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22

Deverson, Edward V., Louise Leong, Angela Seelig, W. John Coadwell, Evelyn M. Tredgett, Geoffrey W. Butcher, and Jonathan C. Howard. "Functional Analysis by Site-Directed Mutagenesis of the Complex Polymorphism in Rat Transporter Associated with Antigen Processing." Journal of Immunology 160, no. 6 (March 15, 1998): 2767–79. http://dx.doi.org/10.4049/jimmunol.160.6.2767.

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Abstract The transporter associated with Ag processing, TAP, is an endoplasmic reticulum resident heterodimeric member of the ATP-binding cassette transporter family. TAP transports short peptides from cytosol to the endoplasmic reticulum lumen for loading into recently synthesized class I MHC molecules. In the rat, two alleles of the TAP2 chain differ in their permissiveness to the transport of peptides with small hydrophobic, polar, or charged amino acids at the C terminus, and this correlates with differences between the peptide sets loaded into certain class I molecules in vivo. We have used segmental exchanges and site-directed mutagenesis to identify the residues in rat TAP2 responsible for differential transport between the two alleles of peptides terminating above all in the positively charged residue, arginine. Of the 25 residues by which the two functional TAP2 alleles differ, we have localized differential transport of peptides with a C-terminal arginine to two adjacent clusters of exchanges in the membrane domain involving a total of five amino acids. Each cluster, transferred by site-directed mutagenesis from the permissive to the restrictive sequence, can independently confer on TAP a partial ability to transport peptides with arginine at the C terminus. The results suggest that the permissive TAP2-A allele evolved in at least two steps, each partially permissive for peptides with charged C termini.
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Mitrou, Nicholas, Christopher G. Scully, Branko Braam, Ki H. Chon, and William A. Cupples. "Laser speckle contrast imaging reveals large-scale synchronization of cortical autoregulation dynamics influenced by nitric oxide." American Journal of Physiology-Renal Physiology 308, no. 7 (April 1, 2015): F661—F670. http://dx.doi.org/10.1152/ajprenal.00022.2014.

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Synchronization of tubuloglomerular feedback (TGF) dynamics in nephrons that share a cortical radial artery is well known. It is less clear whether synchronization extends beyond a single cortical radial artery or whether it extends to the myogenic response (MR). We used LSCI to examine cortical perfusion dynamics in isoflurane-anesthetized, male Long-Evans rats. Inhibition of nitric oxide synthases by Nω-nitro-l-arginine methyl ester (l-NAME) was used to alter perfusion dynamics. Phase coherence (PC) was determined between all possible pixel pairs in either the MR or TGF band (0.09–0.3 and 0.015–0.06 Hz, respectively). The field of view (≈4 × 5 mm) was segmented into synchronized clusters based on mutual PC. During the control period, the field of view was often contained within one cluster for both MR and TGF. PC was moderate for TGF and modest for MR, although significant in both. In both MR and TGF, PC exhibited little spatial variation. After l-NAME, the number of clusters increased in both MR and TGF. MR clusters became more strongly synchronized while TGF clusters showed small highly coupled, high-PC regions that were coupled with low PC to the remainder of the cluster. Graph theory analysis probed modularity of synchronization. It confirmed weak synchronization of MR during control that probably was not physiologically relevant. It confirmed extensive and long-distance synchronization of TGF during control and showed increased modularity, albeit with larger modules seen in MR than in TGF after l-NAME. The results show widespread synchronization of MR and TGF that is differentially affected by nitric oxide.
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Lin, Jianwei, Murray S. R. Smith, Bernard E. Tuch, David A. Walsh, and Danny K. Y. Wong. "Detection of NO at Small Carbon Electrodes as a Means to Assess the Inhibition Efficiency in its Release from Foetal Pig Islet-Like Cell Clusters." Australian Journal of Chemistry 56, no. 3 (2003): 167. http://dx.doi.org/10.1071/ch02204.

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As a xenotransplant, foetal pig islet-like cell clusters (ICCs) are tissues with a potential to reverse hyperglycaemia in Type I diabetes. Following the exposure of ICCs to some pro-inflammatory cytokine factors, the amino acid L-arginine is catalytically cleaved into NO. A cascade of events is then triggered by the NO, leading to tissue apoptosis. In our laboratory, N-monomethyl-L-arginine (an antagonist of NO formation) and heat shock treatment (an inhibitor of NO synthetic enzyme) have been used to prevent pathological injuries in cytokine-induced ICCs. Chronoamperometry at Nafion-coated carbon cylinder electrodes (<5 µm tip diameter) adjacent to cytokine-induced ICCs was employed in this study to periodically monitor NO release and diffusion in ICCs, so that the inhibition efficiency of the respective treatments could be evaluated. Using cytokine-induced ICCs with L-arginine, the electrode recorded a current increase, arising from the oxidation of released NO, over a period of 30 min, followed by a current plateau that persisted for 3 h. In contrast, no corresponding current increase was observed in control experiments involving non-cytokine-induced ICCs with L-arginine, demonstrating the reliability of the direct detection of NO at the carbon electrodes. When the cells were subjected to N-monomethyl-L-arginine or mild heat shock pre-treatment, a decrease in the oxidation current of released NO was observed, demonstrating their inhibitive role in down-regulating NO generation and release.
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25

Gettins, Peter G. W., and Klavs Dolmer. "A proximal pair of positive charges provides the dominant ligand-binding contribution to complement-like domains from the LRP (low-density lipoprotein receptor-related protein)." Biochemical Journal 443, no. 1 (March 14, 2012): 65–73. http://dx.doi.org/10.1042/bj20111867.

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The LRP (low-density lipoprotein receptor-related protein) can bind a wide range of structurally diverse ligands to regions composed of clusters of ~40 residue Ca2+-dependent, disulfide-rich, CRs (complement-like repeats). Whereas lysine residues from the ligands have been implicated in binding, there has been no quantification of the energetic contributions of such interactions and hence of their relative importance in overall affinity, or of the ability of arginine or histidine residues to bind. We have used four representative CR domains from the principal ligand-binding cluster of LRP to determine the energetics of interaction with well-defined small ligands that include methyl esters of lysine, arginine, histidine and aspartate, as well as N-terminally blocked lysine methyl ester. We found that not only lysine but also arginine and histidine bound well, and when present with an additional proximal positive charge, accounted for about half of the total binding energy of a protein ligand such as PAI-1 (plasminogen activator inhibitor-1). Two such sets of interactions, one to each of two CR domains could thus account for almost all of the necessary binding energy of a real ligand such as PAI-1. For the CR domains, a central aspartate residue in the sequence DxDxD tightens the Kd by ~20-fold, whereas DxDDD is no more effective. Together these findings establish the rules for determining the binding specificity of protein ligands to LRP and to other LDLR (low-density lipoprotein receptor) family members.
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26

Kern, A., K. Schmidt, C. Leder, O. J. Müller, C. E. Wobus, K. Bettinger, C. W. Von der Lieth, J. A. King, and J. A. Kleinschmidt. "Identification of a Heparin-Binding Motif on Adeno-Associated Virus Type 2 Capsids." Journal of Virology 77, no. 20 (October 15, 2003): 11072–81. http://dx.doi.org/10.1128/jvi.77.20.11072-11081.2003.

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ABSTRACT Infection of cells with adeno-associated virus (AAV) type 2 (AAV-2) is mediated by binding to heparan sulfate proteoglycan and can be competed by heparin. Mutational analysis of AAV-2 capsid proteins showed that a group of basic amino acids (arginines 484, 487, 585, and 588 and lysine 532) contribute to heparin and HeLa cell binding. These amino acids are positioned in three clusters at the threefold spike region of the AAV-2 capsid. According to the recently resolved atomic structure for AAV-2, arginines 484 and 487 and lysine 532 on one site and arginines 585 and 588 on the other site belong to different capsid protein subunits. These data suggest that the formation of the heparin-binding motifs depends on the correct assembly of VP trimers or even of capsids. In contrast, arginine 475, which also strongly reduces heparin binding as well as viral infectivity upon mutation to alanine, is located inside the capsid structure at the border of adjacent VP subunits and most likely influences heparin binding indirectly by disturbing correct subunit assembly. Computer simulation of heparin docking to the AAV-2 capsid suggests that heparin associates with the three basic clusters along a channel-like cavity flanked by the basic amino acids. With few exceptions, mutant infectivities correlated with their heparin- and cell-binding properties. The tissue distribution in mice of recombinant AAV-2 mutated in R484 and R585 indicated markedly reduced infection of the liver, compared to infection with wild-type recombinant AAV, but continued infection of the heart. These results suggest that although heparin binding influences the infectivity of AAV-2, it seems not to be necessary.
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He, Jinzhi, Geelsu Hwang, Yuan Liu, Lizeng Gao, LaTonya Kilpatrick-Liverman, Peter Santarpia, Xuedong Zhou, and Hyun Koo. "l-Arginine Modifies the Exopolysaccharide Matrix and Thwarts Streptococcus mutans Outgrowth within Mixed-Species Oral Biofilms." Journal of Bacteriology 198, no. 19 (May 9, 2016): 2651–61. http://dx.doi.org/10.1128/jb.00021-16.

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ABSTRACTl-Arginine, a ubiquitous amino acid in human saliva, serves as a substrate for alkali production by arginolytic bacteria. Recently, exogenousl-arginine has been shown to enhance the alkalinogenic potential of oral biofilm and destabilize its microbial community, which might help control dental caries. However,l-arginine exposure may inflict additional changes in the biofilm milieu when bacteria are growing under cariogenic conditions. Here, we investigated how exogenousl-arginine modulates biofilm development using a mixed-species model containing both cariogenic (Streptococcus mutans) and arginolytic (Streptococcus gordonii) bacteria in the presence of sucrose. We observed that 1.5% (wt/vol)l-arginine (also a clinically effective concentration) exposure suppressed the outgrowth ofS. mutans, favoredS. gordoniidominance, and maintainedActinomyces naeslundiigrowth within biofilms (versus vehicle control). In parallel, topicall-arginine treatments substantially reduced the amounts of insoluble exopolysaccharides (EPS) by >3-fold, which significantly altered the three-dimensional (3D) architecture of the biofilm. Intriguingly,l-arginine repressedS. mutansgenes associated with insoluble EPS (gtfB) and bacteriocin (SMU.150) production, whilespxBexpression (H2O2production) byS. gordoniiincreased sharply during biofilm development, which resulted in higher H2O2levels in arginine-treated biofilms. These modifications resulted in a markedly defective EPS matrix and areas devoid of any bacterial clusters (microcolonies) on the apatitic surface, while thein situpH values at the biofilm-apatite interface were nearly one unit higher in arginine-treated biofilms (versus the vehicle control). Our data reveal new biological properties ofl-arginine that impact biofilm matrix assembly and the dynamic microbial interactions associated with pathogenic biofilm development, indicating the multiaction potency of this promising biofilm disruptor.IMPORTANCEDental caries is one of the most prevalent and costly infectious diseases worldwide, caused by a biofilm formed on tooth surfaces. Novel strategies that compromise the ability of virulent species to assemble and maintain pathogenic biofilms could be an effective alternative to conventional antimicrobials that indiscriminately kill other oral species, including commensal bacteria.l-Arginine at 1.5% has been shown to be clinically effective in modulating cariogenic biofilms via alkali production by arginolytic bacteria. Using a mixed-species ecological model, we show new mechanisms by whichl-arginine disrupts the process of biofilm matrix assembly and the dynamic microbial interactions that are associated with cariogenic biofilm development, without impacting the bacterial viability. These results may aid in the development of enhanced methods to control biofilms usingl-arginine.
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Turov, V. V., V. M. Gun'ko, and T. V. Krupska. "Methane adsorption onto silicas with various degree of hydrophobicity." Surface 13(28) (December 30, 2021): 94–126. http://dx.doi.org/10.15407/surface.2021.13.094.

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The methane adsorption onto a hydrated surface of hydrophobic silica AM1 alone and impregnated by arginine, and silica gel Si-100 has been studied using low-temperature 1H NMR spectroscopy. It has been shown that the methane adsorption onto the AM1 surface depends on the degree of hydration and pretreatment type. The maximum adsorption (up to 80 mg/g) is observed for a sample hydrated after complete drying. It has been established that the adsorption is determined by a number of clusters of bound water of small radii. Based on a shape of the temperature dependence of the adsorption, it has been assumed that not only physical adsorption occurs, but also the quasi-solid methane hydrates are formed. It has been established that the amount of methane adsorbed onto a surface of a composite system AM1/arginine under isobaric conditions increases by tens of times (from 0.5 to 80 mg/g) in the presence of pre-adsorbed water pre-adsorbed at the surface. Probable mechanisms of the methane adsorption are physical adsorption on a surface, condensation in narrow voids between silica nanoparticles and nano-scaled (1-10 nm) water clusters, and the formation of solid (clathrate) methane hydrates. Water, adsorbed at a surface in a wide range of hydration, forms various clusters. This water is mainly strongly associated and characterized by chemical shifts in the range dH = 4-6 ppm. The hydrate structures with methane/water are quite stable and can exist even in the chloroform medium. However, in this case, a part of water transforms into a weakly associated state and it is observed at dH = 1.5-2 ppm.
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29

Adams, William M., Michael Wininger, Mitchell E. Zaplatosch, Derek J. Hevel, Jaclyn P. Maher, and Jared T. McGuirt. "Influence of Nutrient Intake on 24 Hour Urinary Hydration Biomarkers Using a Clustering-Based Approach." Nutrients 12, no. 10 (September 25, 2020): 2933. http://dx.doi.org/10.3390/nu12102933.

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Previous work focusing on understanding nutrient intake and its association with total body water homeostasis neglects to consider the collinearity of types of nutrients consumed and subsequent associations with hydration biomarkers. Therefore, the purpose of this study was to analyze consumption patterns of 23 a priori selected nutrients involved in osmotic homeostasis, as well as their association with 24 h urinary hydration markers among fifty African–American first-year college students through a repeated measures observation in a daily living setting. Through application of hierarchical clustering, we were able to identity four clusters of nutrients based on 24 h dietary recalls: (1) alcohol + pinitol, (2) water + calcium + magnesium + erythritol + inositol + sorbitol + xylitol, (3) total calories + total fat + total protein + potassium + sodium + zinc + phosphorous + arginine, and (4) total carbohydrates + total fiber + soluble fiber + insoluble fiber + mannitol + betaine. Furthermore, we found that consumption of nutrients in Cluster #2 was significantly predictive of urine osmolality (p = 0.004); no other clusters showed statistically significant associations with 24 h urinary hydration biomarkers. We conclude that there may be some nutrients that are commonly consumed concomitantly (at the day level), across a variety of settings and populations, and that a limited subset of the clustering of these nutrients may associate with body water status.
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30

Ye, L., Z. Wu, M. Eleftheriou, and R. Zhou. "Single-mutation-induced stability loss in protein lysozyme." Biochemical Society Transactions 35, no. 6 (November 23, 2007): 1551–57. http://dx.doi.org/10.1042/bst0351551.

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Recent NMR experiments have revealed that a single residue mutation W62G on protein hen's-egg white lysozyme can cause a dramatic loss of long-range interactions and protein stability; however, the molecular mechanism for this surprising phenomenon is not completely clear. In this mini-review, we have summarized some of our recent work on the molecular mechanism with large-scale molecular modelling, and also utilized a new wavelet method to analyse the local structural clusters present in both the wild-type and mutant folding trajectories. These extensive MD (Molecular Dynamics) simulations (10+ μs) were performed in 8 M urea, mimicking the experimental condition. Detailed analyses revealed that the Trp62 residue is the key to a co-operative long-range interaction within the wild-type protein: it acts as a bridge between neighbouring basic residues, mainly arginine residues, through π-type hydrogen bonds or π-cation interactions to form an Arg-Trp-Arg ‘sandwich-like’ local structure. The local cluster near Trp62 further extends its interaction to other clusters, such as the one near Trp111, through Arg112, which is involved in such an Arg-Trp-Arg bridging structure, thus achieving the long-range interactions for the wild-type. On the other hand, the mutant does not have this bridging effect and forms much less local clusters or contacts, and therefore results in a much less stable structure. Overall, these findings not only support the general conclusions of the experiment, but also provide a detailed but somewhat different molecular picture of the disruption of the long-range interactions.
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31

Vagenende, Vincent, Alvin X. Han, Monika Mueller, and Bernhardt L. Trout. "Protein-Associated Cation Clusters in Aqueous Arginine Solutions and Their Effects on Protein Stability and Size." ACS Chemical Biology 8, no. 2 (November 15, 2012): 416–22. http://dx.doi.org/10.1021/cb300440x.

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32

Ohtsuki, Kenzo, Yukihiro Nishikawa, Hitoshi Saito, Hiroshi Munakata, and Toyoki Kato. "DNA-binding sperm proteins with oligo-arginine clusters function as potent activators for egg CK-II." FEBS Letters 378, no. 2 (January 8, 1996): 115–20. http://dx.doi.org/10.1016/0014-5793(95)01424-1.

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33

Holloman, Bryan L., Mitzi Nagarkatti, Prakash Nagarkatti, and Kiesha Wilson. "Single-cell RNA Sequencing Reveals Heterogeneity Amongst Immune Cell Subpopulations in LPS-Induced ALI Mice treated with I3C." Journal of Immunology 206, no. 1_Supplement (May 1, 2021): 13.09. http://dx.doi.org/10.4049/jimmunol.206.supp.13.09.

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Abstract Traditionally, macrophage M1-vs-M2 dichotomy have remained fundamentally unchanged since their identification. The oversimplification of immune cell subpopulations using flow cytometric analysis fails to capture the full heterogeneity of these cells in response to disease state and treatment. However, single-cell RNA sequencing (sc-RNAseq) serves as a diagnostic tool that clusters cells based on the whole transcriptomics of individual cells, without the limitation of surface markers and transcriptional factors. In the current study, we aimed to better understand the immunomodulatory mechanism of indole-3-carbinol (I3C) on cell state. To that end, 5mg/kg of LPS was intranasally injected in C57BL/6 mice to induce ALI, and the mice were treated with 80mg/kg I3C three hours after disease induction. After 72 hours mice were euthanized. Whole lung cells were utilized for flow cytometry and sc-RNAseq. Strikingly, the traditional M1-vs-M2 separation was inadequate in classifying all macrophage clusters. LPS+I3C treated-mice had a decrease in Isg15, Ccl5, and Ly6c2 expression in M1 cluster; genes linked to inflammation. Also, the expression of monocyte chemoattractant genes (Cxcl2 and Cxcl3), arginine-associated transport gene (Slc7ac), and major histocompatibility complex (MHC) genes (H2-Ab1 and H2-K1) in M2 cluster was decreased in the diseased group following I3C treatment. In conclusion, several alterations in gene expression in myeloid immune cell subpopulations were identified following treatment with indole-3-carbinol. Thus, shedding light on several new macrophage subpopulations not identified using traditional flow cytometric analysis may offer novel mechanistic insights into disease induction.
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34

Tolo, Isaiah, Jonathan C. Thomas, Rebecca S. B. Fischer, Eric L. Brown, Barry M. Gray, and D. Ashley Robinson. "Do Staphylococcus epidermidis Genetic Clusters Predict Isolation Sources?" Journal of Clinical Microbiology 54, no. 7 (April 13, 2016): 1711–19. http://dx.doi.org/10.1128/jcm.03345-15.

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Staphylococcus epidermidisis a ubiquitous colonizer of human skin and a common cause of medical device-associated infections. The extent to which the population genetic structure ofS. epidermidisdistinguishes commensal from pathogenic isolates is unclear. Previously, Bayesian clustering of 437 multilocus sequence types (STs) in the international database revealed a population structure of six genetic clusters (GCs) that may reflect the species' ecology. Here, we first verified the presence of six GCs, including two (GC3 and GC5) with significant admixture, in an updated database of 578 STs. Next, a single nucleotide polymorphism (SNP) assay was developed that accurately assigned 545 (94%) of 578 STs to GCs. Finally, the hypothesis that GCs could distinguish isolation sources was tested by SNP typing and GC assignment of 154 isolates from hospital patients with bacteremia and those with blood culture contaminants and from nonhospital carriage. GC5 was isolated almost exclusively from hospital sources. GC1 and GC6 were isolated from all sources but were overrepresented in isolates from nonhospital and infection sources, respectively. GC2, GC3, and GC4 were relatively rare in this collection. No association was detected betweenfdh-positive isolates (GC2 and GC4) and nonhospital sources. Using a machine learning algorithm, GCs predicted hospital and nonhospital sources with 80% accuracy and predicted infection and contaminant sources with 45% accuracy, which was comparable to the results seen with a combination of five genetic markers (icaA, IS256,sesD[bhp],mecA, and arginine catabolic mobile element [ACME]). Thus, analysis of population structure with subgenomic data shows the distinction of hospital and nonhospital sources and the near-inseparability of sources within a hospital.
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Tuch, Bernard E., Jocelyn C. Madrid, Ellie Summers, and Murray S. R. Smith. "Production and Characterization of Fetal Sheep Pancreatic Islet-Like Cell Clusters." Cell Transplantation 5, no. 4 (July 1996): 491–98. http://dx.doi.org/10.1177/096368979600500408.

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Explants of fetal sheep pancreas transplanted into diabetic athymic mice survive for many months but there is only partial differentiation of the endocrine cells. As an alternative form of graft we examined the possibility of creating islet-like cell clusters (ICCs) by collagenase digestion of the fetal sheep pancreas, as has been described for human and porcine fetal pancreas. Such ICCs did form at the rate of 6-23 per 10 mg pancreas; their size varied between 65 and 474 μm (median 232 μm) and their insulin content was 1.6 ± 0.2 mU per 20 ICCs. Laser scanning confocal analysis showed that 4.6 ± 0.7% of the cells contained insulin. Insulin was secreted from ICCs maintained in culture at the daily rate of 2.5 mU per 30 ICCs. Arginine but not glucose or theophylline enhanced acute insulin secretion in vitro. Transplantation of up to 1000 ICCs into athymic and scid mice resulted in sparse growth of the epithelial-like cells in the graft and only partial differentiation of the endocrine cells. Hyperglycaemia in diabetic recipients was not normalized. Thus, while functioning ICCs can be created from fetal sheep pancreas, they do not appear to be appropriate for transplantation to reverse diabetes in mice.
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36

Sacco-Bubulya, Paula, and David L. Spector. "Disassembly of interchromatin granule clusters alters the coordination of transcription and pre-mRNA splicing." Journal of Cell Biology 156, no. 3 (February 4, 2002): 425–36. http://dx.doi.org/10.1083/jcb.200107017.

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To examine the involvement of interchromatin granule clusters (IGCs) in transcription and pre-mRNA splicing in mammalian cell nuclei, the serine-arginine (SR) protein kinase cdc2-like kinase (Clk)/STY was used as a tool to manipulate IGC integrity in vivo. Both immunofluorescence and transmission electron microscopy analyses of cells overexpressing Clk/STY indicate that IGC components are completely redistributed to a diffuse nuclear localization, leaving no residual structure. Conversely, overexpression of a catalytically inactive mutant, Clk/STY(K190R), causes retention of hypophosphorylated SR proteins in nuclear speckles. Our data suggest that the protein–protein interactions responsible for the clustering of interchromatin granules are disrupted when SR proteins are hyperphosphorylated and stabilized when SR proteins are hypophosphorylated. Interestingly, cells without intact IGCs continue to synthesize nascent transcripts. However, both the accumulation of splicing factors at sites of pre-mRNA synthesis as well as pre-mRNA splicing are dramatically reduced, demonstrating that IGC disassembly perturbs coordination between transcription and pre-mRNA splicing in mammalian cell nuclei.
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37

Beatch, Martin D., Jason C. Everitt, LokMan J. Law, and Tom C. Hobman. "Interactions between Rubella Virus Capsid and Host Protein p32 Are Important for Virus Replication." Journal of Virology 79, no. 16 (August 15, 2005): 10807–20. http://dx.doi.org/10.1128/jvi.79.16.10807-10820.2005.

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ABSTRACT The distribution and morphology of mitochondria are dramatically affected during infection with rubella virus (RV). Expression of the capsid, in the absence of other viral proteins, was found to induce both perinuclear clustering of mitochondria and the formation of electron-dense intermitochondrial plaques, both hallmarks of RV-infected cells. We previously identified p32, a host cell mitochondrial matrix protein, as a capsid-binding protein. Here, we show that two clusters of arginine residues within capsid are required for stable binding to p32. Mutagenic ablation of the p32-binding site in capsid resulted in decreased mitochondrial clustering, indicating that interactions with this cellular protein are required for capsid-dependent reorganization of mitochondria. Recombinant viruses encoding arginine-to-alanine mutations in the p32-binding region of capsid exhibited altered plaque morphology and replicated to lower titers. Further analysis indicated that disruption of stable interactions between capsid and p32 was associated with decreased production of subgenomic RNA and, consequently, infected cells produced significantly lower amounts of viral structural proteins under these conditions. Together, these results suggest that capsid-p32 interactions are important for nonstructural functions of capsid that include regulation of virus RNA replication and reorganization of mitochondria during infection.
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Coffey, A. K., D. J. O'Sullivan, S. Homma, T. P. Dousa, and H. Valtin. "Induction of intramembranous particle clusters in mice with nephrogenic diabetes insipidus." American Journal of Physiology-Renal Physiology 261, no. 4 (October 1, 1991): F640—F646. http://dx.doi.org/10.1152/ajprenal.1991.261.4.f640.

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In mice with hereditary nephrogenic diabetes insipidus (NDI), the inability of vasopressin to increase hydraulic water permeability is reflected in a lack of intramembranous particle (IMP) clusters in apical membranes of inner medullary collecting ducts. The lack arises from anomalously high activity of one or two isozymes of adenosine 3',5'-cyclic monophosphate-phosphodiesterase (cAMP-PDE). We asked whether inhibition of these isozymes with rolipram and cilostamide would raise not only the tissue content of cAMP but also and simultaneously restore IMP clusters. Inner medullary collecting ducts from NDI mice were incubated in vitro. Tissue content of cAMP (fmol of cAMP per bundle) and number of IMP clusters (per 100 microns 2 of principal cell apical membrane) were, respectively: control, 44.8 +/- 13.0 and 4.16 +/- 1.49; arginine vasopressin (AVP), 31.7 +/- 8.0 and 3.98 +/- 1.56; rolipram and cilostamide, 109.7 +/- 21.0 and 58.09 +/- 15.74; and AVP plus rolipram and cilostamide, 305.7 +/- 75 and 48.63 +/- 11.03 (with the last four values showing significant difference from control and AVP only, respectively). In addition, treating NDI mice with rolipram and cilostamide in vivo reduced their high fluid turnover. We conclude that failure by AVP to increase cAMP in cells of collecting ducts, which results from anomalously high activity of one or two specific isozymes of cAMP-PDE, is the major or sole cause for the excretion of hypotonic urine in NDI mice (DI +/+ Severe strain).
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39

Nützmann, Hans-Wilhelm, Juliane Fischer, Kirstin Scherlach, Christian Hertweck, and Axel A. Brakhage. "Distinct Amino Acids of Histone H3 Control Secondary Metabolism in Aspergillus nidulans." Applied and Environmental Microbiology 79, no. 19 (July 26, 2013): 6102–9. http://dx.doi.org/10.1128/aem.01578-13.

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ABSTRACTChromatin remodelling events play an important role in the secondary metabolism of filamentous fungi. Previously, we showed that a bacterium,Streptomyces rapamycinicus, is able to reprogram the histone-modifying Spt-Ada-Gcn5-acetyltransferase/ADA (SAGA/ADA) complex of the model fungusAspergillus nidulans. Consequently, the histone H3 amino acids lysine 9 and lysine 14 at distinct secondary metabolism genes were specifically acetylated during the bacterial fungal interaction, which, furthermore, was associated with the activation of the otherwise silent orsellinic acid gene cluster. To investigate the importance of the histone modifications for distinct gene expression profiles in fungal secondary metabolism, we exchanged several amino acids of histone H3 ofA. nidulans. These amino acids included lysine residues 9, 14, 18, and 23 as well as serine 10 and threonine 11. Lysine residues were replaced by arginine or glutamine residues, and serine/threonine residues were replaced by alanine. All generated mutant strains were viable, allowing direct analysis of the consequences of missing posttranslational histone modifications. In the mutant strains, major changes in the expression patterns at both the transcriptional and metabolite levels of the penicillin, sterigmatocystin, and orsellinic acid biosynthesis gene clusters were detected. These effects were due mainly to the substitution of the acetylatable lysine 14 of histone H3 and were enhanced in a lysine 14/lysine 9 double mutant of histone H3. Taken together, our findings show a causal linkage between the acetylation of lysine residue 14 of histone H3 and the transcription and product formation of secondary metabolite gene clusters.
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40

Kinsel, Gary R., Qingchun Zhao, Jayakumar Narayanasamy, Faten Yassin, H. V. Rasika Dias, Bradley Niesner, Katherine Prater, Chris St. Marie, Le Ly, and Dennis S. Marynick. "Arginine/2,5-Dihydroxybenzoic Acid Clusters: An Experimental and Computational Study of the Gas-Phase and Solid-State Systems†." Journal of Physical Chemistry A 108, no. 15 (April 2004): 3153–61. http://dx.doi.org/10.1021/jp031207s.

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41

Dahl, J., U. Thathamangalam, R. Freund, and T. L. Benjamin. "Functional asymmetry of the regions juxtaposed to the membrane-binding sequence of polyomavirus middle T antigen." Molecular and Cellular Biology 12, no. 11 (November 1992): 5050–58. http://dx.doi.org/10.1128/mcb.12.11.5050-5058.1992.

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The functional importance of the two clusters of positively charged amino acids which flank the hydrophobic membrane-anchoring sequence of polyomavirus middle T (mT) protein has been investigated by using site-directed mutagenesis. A clear asymmetry was apparent. No effect on transformation was seen following multiple alterations or complete removal of the cluster at the carboxyl end of the protein. In contrast, a single substitution replacing the first arginine amino terminal to the hydrophobic stretch with glutamic acid, but not with lysine, histidine, or methionine, produced a partially transformation-defective mutant with a novel phenotype. This mutant failed to confer anchorage-independent growth on F111 established rat embryo fibroblasts but induced foci with altered morphology compared with wild-type mT. Biochemical studies on this mutant revealed that F111 clones expressing levels of mutant mT equivalent to those of wild-type controls showed a 65% reduction in pp60c-src activation and an 87% reduction in mT-associated phosphatidylinositol 3-kinase activity. However, F111 clones expressing seven times more mutant mT than did wild-type controls showed equal or greater levels of kinase activities yet remained incompletely transformed. Possible mechanisms involving this transformation-sensitive region of mT are discussed.
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42

Dahl, J., U. Thathamangalam, R. Freund, and T. L. Benjamin. "Functional asymmetry of the regions juxtaposed to the membrane-binding sequence of polyomavirus middle T antigen." Molecular and Cellular Biology 12, no. 11 (November 1992): 5050–58. http://dx.doi.org/10.1128/mcb.12.11.5050.

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The functional importance of the two clusters of positively charged amino acids which flank the hydrophobic membrane-anchoring sequence of polyomavirus middle T (mT) protein has been investigated by using site-directed mutagenesis. A clear asymmetry was apparent. No effect on transformation was seen following multiple alterations or complete removal of the cluster at the carboxyl end of the protein. In contrast, a single substitution replacing the first arginine amino terminal to the hydrophobic stretch with glutamic acid, but not with lysine, histidine, or methionine, produced a partially transformation-defective mutant with a novel phenotype. This mutant failed to confer anchorage-independent growth on F111 established rat embryo fibroblasts but induced foci with altered morphology compared with wild-type mT. Biochemical studies on this mutant revealed that F111 clones expressing levels of mutant mT equivalent to those of wild-type controls showed a 65% reduction in pp60c-src activation and an 87% reduction in mT-associated phosphatidylinositol 3-kinase activity. However, F111 clones expressing seven times more mutant mT than did wild-type controls showed equal or greater levels of kinase activities yet remained incompletely transformed. Possible mechanisms involving this transformation-sensitive region of mT are discussed.
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43

Wessolowski, A., M. Bienert, and M. Dathe. "Antimicrobial activity of arginine- and tryptophan-rich hexapeptides: the effects of aromatic clusters, d-amino acid substitution and cyclization." Journal of Peptide Research 64, no. 4 (October 2004): 159–69. http://dx.doi.org/10.1111/j.1399-3011.2004.00182.x.

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44

Ogushi, Yuji, Hiroshi Mochida, Takashi Nakakura, Masakazu Suzuki, and Shigeyasu Tanaka. "Immunocytochemical and Phylogenetic Analyses of an Arginine Vasotocin-Dependent Aquaporin, AQP-h2K, Specifically Expressed in the Kidney of the Tree Frog, Hyla japonica." Endocrinology 148, no. 12 (December 1, 2007): 5891–901. http://dx.doi.org/10.1210/en.2007-0613.

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Water movement occurs across the plasma membrane of various cells of animals, plants, and microorganisms through specialized water-channel proteins called aquaporins (AQPs). We have identified a new member of the amphibian AQP family, AQP-h2K, from the kidneys of Hyla japonica. This protein consists of 280 amino acid residues with two NPA (Asn-Pro-Ala) sequence motifs and a mercury-sensitive cysteine residue just upstream from the second NPA motif. There are two putative N-linked glycosylation sites at Asn-120 and Asn-128 and one protein kinase A phosphorylation site at Ser-262. The AQP-h2K protein was specifically expressed in the apical membrane and/or cytoplasm of principal cells in the kidney collecting ducts. After stimulation with arginine vasotocin, it was translocated from the cytoplasmic pool to the apical membrane. Phylogenetic analysis of AQP proteins from anurans and mammals identified six clusters of anuran AQPs: types 1, 2, 3, and 5 and two anuran-specific types, designated a1 and a2. The cluster AQPa2 contains Hyla AQP-h2 and AQP-h3, which are expressed in the anuran urinary bladder and ventral pelvic skin. AQP-h2K belongs to the type 2, together with mammalian (human and mouse) AQP2, suggesting that AQP-h2K is an anuran ortholog of the neurohypophysial hormone-regulated mammalian AQP2 and that the AQP2 molecule is already present in the anuran mesonephros.
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45

Maillard, Julien, Pierre Genevaux, and Christof Holliger. "Redundancy and specificity of multiple trigger factor chaperones in Desulfitobacteria." Microbiology 157, no. 8 (August 1, 2011): 2410–21. http://dx.doi.org/10.1099/mic.0.050880-0.

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The ribosome-bound trigger factor (TF) chaperone assists folding of newly synthesized polypeptides and participates in the assembly of macromolecular complexes. In the present study we showed that multiple distinct TF paralogues are present in genomes of Desulfitobacteria, a bacterial genus known for its ability to grow using organohalide respiration. Two full-length TF chaperones and at least one truncated TF (lacking the N-terminal ribosome-binding domain) were identified, the latter being systematically linked to clusters of reductive dehalogenase genes encoding the key enzymes in organohalide respiration. Using a well-characterized heterologous chaperone-deficient Escherichia coli strain lacking both TF and DnaK chaperones, we demonstrated that all three TF chaperones were functional in vivo, as judged by their ability to partially suppress bacterial growth defects and protein aggregation in the absence of both major E. coli chaperones. Next, we found that the N-terminal truncated TF-like protein PceT functions as a dedicated chaperone for the cognate reductive dehalogenase PceA by solubilizing and stabilizing it in the heterologous system. Finally, we showed that PceT specifically interacts with the twin-arginine signal peptide of PceA. Taken together, our data define PceT (and more generally the new RdhT family) as a class of TF-like chaperones involved in the maturation of proteins secreted by the twin-arginine translocation pathway.
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46

OTONKOSKI, TIMO. "Insulin and Glucagon Secretory Responses to Arginine, Glue agon, and Theophylline During Perifusion of Human Fetal Islet-Like Cell Clusters*." Journal of Clinical Endocrinology & Metabolism 67, no. 4 (October 1988): 734–40. http://dx.doi.org/10.1210/jcem-67-4-734.

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47

Ivanov, Ivan G., Adriana A. Saraffova, and Mounir G. Abouhaidar. "Unusual effect of clusters of rare arginine (AGG) codons on the expression of human interferon α1 gene in Escherichia Coli." International Journal of Biochemistry & Cell Biology 29, no. 4 (April 1997): 659–66. http://dx.doi.org/10.1016/s1357-2725(96)00161-6.

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48

Schmitt, Christine, Jayesh Arun Bafna, Benedikt Schmid, Stefan Klingl, Steffen Baier, Birgit Hemmis, Richard Wagner, Mathias Winterhalter, and Lars M. Voll. "Manipulation of charge distribution in the arginine and glutamate clusters of the OmpG pore alters sugar specificity and ion selectivity." Biochimica et Biophysica Acta (BBA) - Biomembranes 1861, no. 10 (October 2019): 183021. http://dx.doi.org/10.1016/j.bbamem.2019.07.009.

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49

Brown, D., G. I. Shields, H. Valtin, J. F. Morris, and L. Orci. "Lack of intramembranous particle clusters in collecting ducts of mice with nephrogenic diabetes insipidus." American Journal of Physiology-Renal Physiology 249, no. 4 (October 1, 1985): F582—F589. http://dx.doi.org/10.1152/ajprenal.1985.249.4.f582.

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We suggested previously, on the basis of indirect evidence, that in two strains of mice with nephrogenic defects of urinary concentration the deficiency arose from an inadequate rise in water permeability of the collecting duct system. In this study we tested the question further by assuming that the frequency of intramembranous particle (IMP) clusters seen by freeze-fracture can be used as a morphological marker of vasopressin-induced water permeability. Three genotypes of mice were studied: 1) DI +/+ Severe, with florid, vasopressin-resistant diabetes insipidus; 2) DI +/+ Nonsevere, with an intermediate deficiency of urinary concentration; and 3) normal, VII +/+ mice. In addition, we examined a group of DI +/+ Severe mice that had been injected with exogenous 1-desamino-8-D-arginine vasopressin (DDAVP) subcutaneously for 3 days. Since the results in this group did not differ from those in untreated DI +/+ Severe mice, all data for this genotype were combined. IMP clusters within luminal membranes of inner medullary collecting duct principal cells were quantified by freeze-fracture electron microscopy. Urinary osmolality and percentage of cells showing clusters were, respectively: 203 +/- 43 mosmol/kg H2O and 0% in DI +/+ Severe mice; 1,133 +/- 86 and 33 +/- 4 in DI +/+ Nonsevere mice; and 2,234 +/- 190 and 52 +/- 5 in VII +/+ animals. With the exception of one animal, there was no overlap of the data, which were significantly different from one another for each variable. We conclude that in DI +/+ Severe mice, both endogenous and exogenous vasopressin are unable to increase the water permeability of medullary collecting ducts.(ABSTRACT TRUNCATED AT 250 WORDS)
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50

Ruzicka, Frank J., Kafryn W. Lieder, and Perry A. Frey. "Lysine 2,3-Aminomutase from Clostridium subterminale SB4: Mass Spectral Characterization of Cyanogen Bromide-Treated Peptides and Cloning, Sequencing, and Expression of the Gene kamA in Escherichia coli." Journal of Bacteriology 182, no. 2 (January 15, 2000): 469–76. http://dx.doi.org/10.1128/jb.182.2.469-476.2000.

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ABSTRACT Lysine 2,3-aminomutase (KAM, EC 5.4.3.2 .) catalyzes the interconversion of l-lysine and l-β-lysine, the first step in lysine degradation in Clostridium subterminale SB4. KAM requires S-adenosylmethionine (SAM), which mediates hydrogen transfer in a mechanism analogous to adenosylcobalamin-dependent reactions. KAM also contains an iron-sulfur cluster and requires pyridoxal 5′-phosphate (PLP) for activity. In the present work, we report the cloning and nucleotide sequencing of the gene kamA for C. subterminale SB4 KAM and conditions for its expression in Escherichia coli. The cyanogen bromide peptides were isolated and characterized by mass spectral analysis and, for selected peptides, amino acid and N-terminal amino acid sequence analysis. PCR was performed with degenerate oligonucleotide primers and C. subterminale SB4 chromosomal DNA to produce a portion of kamA containing 1,029 base pairs of the gene. The complete gene was obtained from a genomic library of C. subterminale SB4 chromosomal DNA by use of DNA probe analysis based on the 1,029-base pair fragment. The full-length gene consisted of 1,251 base pairs specifying a protein of 47,030 Da, in reasonable agreement with 47,173 Da obtained by electrospray mass spectrometry of the purified enzyme. N- and C-terminal amino acid analysis of KAM and its cyanogen bromide peptides firmly correlated its amino acid sequence with the nucleotide sequence of kamA. A survey of bacterial genome databases identified seven homologs with 31 to 72% sequence identity to KAM, none of which were known enzymes. An E. coli expression system consisting of pET 23a(+) plus kamA yielded unsatisfactory expression and bacterial growth. Codon usage in kamA includes the use of AGA for all 29 arginine residues. AGA is rarely used in E. coli, and arginine clusters at positions 4 and 5, 25 and 27, and 134, 135, and 136 apparently compound the barrier to expression. Coexpression of E. coli argU dramatically enhanced both cell growth and expression of KAM. Purified recombinant KAM is equivalent to that purified from C. subterminale SB4.
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